Hey @openmindz,
That does help, however we have 400+ instances in question and it seems to happen to around 1% of random instances and at random times (but at least 2 or 3 times throughout the week). We assumed using CheckMK would be the way to go here to be honest, and without ‘bashing’ CheckMK at all (it really is a great product and I’ve been using it for years) it does seem that other products (we would prefer to not use) are able to monitor per process CPU usage out of the box and graph accordingly.
We may well indeed have to script some sort of periodic job that uses nmon or top and dump the statistics to a file on some sort of external storage periodically to get an insight as to what’s going on here (although we were obviously trying to avoid this), but long term it would have been nice to be able to graph the CPU usage of all individual CPU processes anyway.
Thanks for all your help though - very much appreciated! 
James